The Ghost of You
by Invisia
Summary: AU. S3 spoilers. "Sherlock Holmes," she replied softly, not quite meeting his gaze. "I thought you were dead." Sherlock shook his head. "Obviously not," he replied. [...] "What are you doing here?" he asked again, beginning to get impatient. "Hiding," she replied. "Do you want me to leave?" Sherlock thought about it for a moment, before shaking his head. "No."
1. The Absence of You

**A/N: **So, guess who started watching Sherlock this year? And guess who became completely obsessed? Ha. So, anyway, this is my first Sherlock fan-fic. I've tried to get my facts straight as possible, but this is an AU, so I suppose it doesn't matter that much. Sorry for any screwing-up of characters, this is just how I've interpreted them. So, that being said, please enjoy, and let me know what you think!

**The Story behind the Story: **You know those really sad, angsty fics set between TRF and TEH that focus on everyone moping, etc.? Well, I was reading one (Dianne's _I Think I'm Going to Die'_) when it was mentioned about Sherlock being a ghost. So I got curious. Then I started reading something about Molly and Moriarty, and well, this happened.

**Summery: **It's been two years and Sherlock's back, except everybody thought he was dead. Not even his brother knew of his survival. Molly herself had run the autopsy. So how is he still here?

Molly tries not to worry. After all, it's not the first time a dead person has come back to life…

**Disclaimer: **I don't own Sherlock; the BBC does. Also, thank you to Ariane DeVere on livejournal, who's transcrips of the episodes are highly useful. Quotes may be taken from the actual episodes.

* * *

**Chapter One**

**The Absence of You**

* * *

"Will you marry me?" John watched as Mary's smile grew even wider, and she nodded.

"God, yes!" she agreed, laughing. John grinned, and slid the ring onto her finger. It looked right there. It was about time things started looking right again. For the past two years, things had been so wrong.

* * *

Molly stood by the window, peering through a crack in the curtains. She stood just slightly to the side, so that if anyone looked up, they wouldn't see her. In the yellow glow of the streetlight, she couldn't yet see His dark silhouette. She looked up at the clock. It was only eight o'clock. He would be a while yet.

She stepped back a bit, glancing around the darkened flat. For the past two years she had moved around a lot. First she had lost her job, and then He had found her. She'd been downgrading, going from small, grotty places to even smaller, grottier places. She didn't pay the electricity bill, and unless she lit a candle, it was always dark.

This flat had only three rooms. There was the kitchen, the tiny bathroom, and the bedroom, in which she stood now. Her bed was small and single, covered in a simple white quilt and a beige blanket. The wardrobe was made of flimsy wood and cheap plastic, and barely large enough to contain her clothes.

Sometimes she would look back to the life she used to lead and wonder how she ever could have lived that way. How she could have worked happily among corpses, having now seen what she had. How she could have looked at Sherlock Holmes and admired him. He had been genius, but a genius who had put her down. Who had made her feel insignificant.

He was right.

She still admired Sherlock, but not in the way she once had. She respected him, but she wouldn't dare step near him. No, she'd learned her lesson. He claimed to be a sociopath. Maybe he wasn't, maybe he was. She didn't care. She knew now to stay away from people like that. People with no regard for human life.

There was a knock at the door. Taking a deep breath, she pulled on her coat, walked through to the kitchen, and pulled back the bolt. She pressed down on the handle and pulled it towards her, looking down meekly before glancing up at His face.

"Are you ready?" he asked her. She nodded, and followed him outside, not caring to lock the door.

* * *

Mycroft Holmes woke early. He lay in bed for a moment before deducing that he would never get back to sleep now that his brain was fully awake, and pulled himself out of it. He pulled on his dressing gown, slipped on his slippers, and headed from his bedroom into his private sitting room.

He called a maid to make some tea and sat down in his favourite armchair, getting out his laptop and answering his emails. The tea was placed on the table beside the chair, and he periodically took sips from it. Aside from the glow of the laptop screen and a lamp stood behind the chair, the room was dark.

When he felt a sudden chill, Mycroft looked up. The windows were closed, the curtains drawn. So where was that draught coming from? Probably the chimney, he summarized, before seeing something that made him go paler than paper.

Sherlock Holmes smiled at his brother as he stepped into the dim glow of the lamp. "Hello, Brother Mine," he greeted. "Long time no see."

* * *

Molly lay in bed for a long time, staring up at the ceiling. She hadn't slept all night. She often didn't on nights like these. He didn't always show up, and they weren't always out for long, but she could never sleep afterwards. Her brain was always far too awake, replaying images of the evening. Images she'd rather forget.

It had been a graveyard tonight, she remembered, without even meaning to. The same one where they'd buried Sherlock. There had been some kids playing there, barely out of college. They'd been those strange types, the ones who thought they were witches. He'd made her watch as…

No. Not wanting to stay there, alone with her thoughts, any longer, she swung her legs over the side of the bed and got to her feet. There bare floorboards were freezing cold, but it was November, and the heating system in the building wasn't the best. She made her way to the kitchen and put the kettle on to boil. She remembered how she used to spend the mornings. She'd watch the news on telly before going into work at Bart's.

Well, those days were over now. She prepared her tea, which was only ever lukewarm.

* * *

Mycroft sat watching his brother, who had refused tea or coffee, and his offer of food. He looked unchanged from the last time they'd met; same curly hair, hard blue eyes, pale skin and skeletal frame. Sherlock was glancing around the room, no doubt deducing what he could.

"So, you're alive," Mycroft said, trying not to sound distressed. Sherlock turned his head slowly towards him and raised an eyebrow.

"Is that not obvious?"

"Where have you been these past two years?"

"None of your concern, Mycroft," Sherlock replied, his tone clipped. "I'm only here to let you know I'm back." He stood up from his chair, making his way over to the door. "I'll be off to Baker Street now. I think I'll surprise John. Jump out of a cake; who knows?"

"Baker Street?" Mycroft said with a frown. "He's not there any more. He's got on with his life."

Sherlock sniffed, affronted. "What life? I've been away. Where is he now, then?"

"What makes you think I know?"

"So you don't know?"

"No, of course I know!" Mycroft snapped. Sherlock smirked. Mycroft sighed and told his brother the address. Sherlock nodded.

"Well, I'll see you later," he said. "Goodbye." With that, he turned and stalked through the door. Mycroft blinked a couple of times, before shaking his head.

No, his brother didn't just walk through a closed door. He was mistaken. It was dark in here, after all…

* * *

"The famous blog, finally!" Mary exclaimed, grinning at John. John sighed, rubbing his damp face with a towel.

"Come on, that's-"

"Ancient history, I know." Mary's smile drooped slightly as she placed the iPad down on the bed. "Don't worry, I won't read it."

"That's a wise choice. John does tend to over-dramatize things. I doubt that half the stuff on there is even true." Both of them jumped, their heads snapping towards the living room where Sherlock Holmes stood in front of the open window. He looked just like he used to, in his coat and scarf, and that smug, superior expression on his face.

"Hello, John," he greeted, breaking the spell of silence cast upon the room.

* * *

"Hello, Jenna," Molly greeted. Jenny, the other secretary, was big and brawny, and thus made everything in the office look incredibly small. Including Molly.

Molly sat down and logged onto the computer, fixing the headset to her head and waiting for someone to ring. She enjoyed the sound of the keys on the keyboard being tapped by her trembling fingers. It chased away the thoughts from her brain. As did her mundane job. Nine til' five, five days a week. Typical. Usual. Simple. Boring.

Perfect.

* * *

"Look, let's get out of the flat, okay?" Mary said, later that afternoon, when the tension in the room became too high to be bearable. "Let's go for a walk. Some fresh air will do us all good."

As John moved to get up, he didn't move his gaze from Sherlock. His best friend. The man he'd believed to be dead for the last two years.

Alive again.

It was a miracle, but it also misfortune.

After the two-year absence of Sherlock Holmes, it would be hard to welcome him back into life again.

* * *

**A/N: **So, tell me what you think. Good/bad? Anything you want to happen? I have about three chapter of this written so far, so I'm open to suggestions. Well, have a good day or whatever :)

-Invisi


	2. The Meeting of You

**A/N: **Thanks for the reviews and the follows, they mean a lot :) I'm glad you like it so far. Also, if you have any requests for something you want to see/happen, feel free to ask. So, onto chapter two.

**Disclaimer: **I don't own Sherlock; the BBC does. Also, thank you to Ariane DeVere on livejournal, who's transcrips of the episodes are highly useful. Quotes may be taken from the actual episodes.

* * *

**Chapter Two**

**The Meeting of You**

* * *

Molly didn't like to ruin her schedule, except on the few occasions where she uprooted her life and moved away again, in an attempt to escape Him. It never worked, though. He always found her, sooner or later.

Now, though, there was one place she hadn't been in a while that she wanted to visit. Why, she didn't know. However, instead of walking home, she instead took the shortest route she knew of to Baker Street. Mrs Hudson, she knew, hadn't rented out 221B yet. Maybe…

Maybe if she just left everything behind and hid out in the former residence of Sherlock Holmes, nobody would find her. Maybe He would finally leave her be.

Yeah, she thought, sarcastically, bitterly. Right.

* * *

"So, what happened to the flat at Baker Street? And all my stuff?" Sherlock asked as they walked through London. Mary was eating mushy peas from a small polystyrene pot, but Sherlock had declined the offer of eating and and John was too angry to. She had never seen her fiance that mad before.

"It's all still there," John replied. "I spoke to Mrs Hudson the other day- yesterday, in fact." Sherlock nodded.

"That's good. I'll go there now." He set off with a purposeful stride. Mary turned to John, unsure of what entirely was going on.

"Do we follow him?"

"No," John spat. "Let him go off. Who cares? I don't!" He threw his arms in the air in frustration. Mary put a soothing hand on his shoulder. He laughed bitterly. "Can you believe his nerve?" Mary smiled.

The detective hadn't spoken much, and certainly he didn't have an excuse for causing her soon-to-be-husband such grief, but there was something she liked about him. He seemed the type who could keep a secret. Someone who would keep her secret.

"I like him," she replied. John twisted around to face her, frowning.

"What?" Mary shrugged, still smiling.

"I like him."

* * *

Molly heard Mrs Hudson scream downstairs. She winced, curling up in the chair. John's chair, that was; she couldn't abide to sit in Sherlock's.

_Please don't let Him be here. Please don't let Him hurt her because of me_, she prayed, almost begged. She didn't know who to, she just hoped someone would hear her. A moment later the screaming stopped, replaced by chatter, and she sagged in relief. Then she gave a dry laugh.

_Look at you, Molly Hooper. Praying to God now, are we?_ The shook the thought away, but it was only replaced with another, this one speaking in His voice.

_Don't get too big for your boots, honey. Why would I hurt that landlady because of you? You're nothing. You're worthless. If you really wanted me to go away, I would, I'd leave you alone. But then what would you be? A small, lonely, frightened girl, all alone in the big bad world…_

She stifled a sob as she heard feet on the stairs.

* * *

Sherlock pushed open the door to the flat, noting that someone had been in here since he'd left, quite recently, too. John had been in yesterday, he'd been told that, but there were fresher signs of someone entering. And yet no sign of them leaving…

So they were still there.

Mrs Hudson hovered at his shoulder as he stepped into the flat and followed the signs of someone intruding. A moment later, he saw them, sitting on John's chair. It was a woman, probably in her thirties. She was small and pale, completely curled up in the chair, her long, dark blonde hair falling around her face.

"Who are you, and what are you doing in my flat?" he demanded sharply. She looked up, startled, and Sherlock realised that he knew her. "Molly Hooper?" he asked, almost to himself, in confusion.

"Sherlock Holmes," she replied softly, not quite meeting his gaze. "I thought you were dead." Sherlock shook his head.

"Obviously not," he replied. She shook her head.

"No," she said dully.

"What are you doing here?" he asked again, beginning to get impatient.

"Hiding," she replied. "Do you want me to leave?"

Sherlock thought about it for a moment, before shaking his head. "No."

* * *

Sherlock was watching Molly curiously. She stood by the window, just to the side of the crack in the curtains, gazing down at the street. Her pale face was lit up by the yellow glow of the streetlight outside. He frowned.

Last time he had seen Molly Hooper, she had been a somewhat cheerful pathology lab assistant, working at Bart's. She had been healthy, had plenty of friends, and a romantic attachment to him (which he did not return). Nobody of importance, and certainly not a puzzle. Now, though… He began to deduce her.

_cat lover Grief paranoia Nervous scared secretary poor living standards Late Nights nightmares sleeplessness Emotional_

He frowned, turning away and picking up his old phone, which somebody had left on the kitchen side. He fished out the lead and plugged it into charge. Five minutes later, he picked it back up and sent a text.

_I'm back - SH_

* * *

Greg Lestrade held his head in his hands, rubbing his temples. Before him were the pictures of a skeleton, dressed in shabby victorian clothes. It had been found in an old room, not far away from Anderson's new place. Recently, Anderson had really fallen apart, becoming almost obsessed with the theory of Sherlock Holmes being alive.

Well, he wasn't. Sherlock Holmes was dead, for better or for worse. At that moment, his phone beeped, the screen flashing to life. With a frown, he picked it up. What he saw made his heart skip a beat.

_I'm back -SH_

"Shit," he whispered to himself, dialing the number of the one person he owed an apology to.

"Greg? What's going on?" Anderson's voice came through the phone. Lestrade sighed.

"You were right," he informed his college bluntly.

"I'm sorry?"

"Sherlock Holmes is alive."

* * *

He didn't come that night, which was a relief. Sherlock stayed up well past midnight, and Molly fell asleep on John's chair. She drifted off into an uneasy sleep, and woke at four in the morning, sobbing quietly. The lights were out, and Sherlock was no longer in the room. That was good. She couldn't stand it if he saw her cry.

Feeling stiff, she stood up, and made her way over to the window. Her leg ached, and so she limped slightly as she walked. She peeked between the crack in the curtains, and almost jumped out of her skin when she saw Him standing there, beckoning to her. How did he know…?

She gulped, grabbed her coat, and made her way silently downstairs.

* * *

This time they stood at the bank of the Thames. He stood next to her, one arm looped around her shoulders. In the shadows across the water, a large, burly figure was shoving another under the water. The person being drowned was trying to claw their way back up, but to no avail. He smiled at her, pulling her closer. He smelled of expensive aftershave and tobacco. She felt sick.

It wasn't the worst of what she'd seen, though. No, she'd seen far worse. He liked to show her these things, gruesome and grizzly murders that would give her nightmares for weeks. Once she'd seen a man have his stomach sliced open and a lung removed. He'd bled to death. It had taken seven minutes, twenty-three seconds, and she'd stood in the shadows, watching.

That was the one that had made her quit her job at Bart's. That was the murder that haunted her every day and night. That was a sight she would never forget, the one that made her feel faint at the sight of blood.

The worst part of all of it?

This never would have happened if Sherlock Holmes had been alive.

* * *

**A/N: **Review?


	3. The Assisting of You

**A/N: **Fun fact: if I put my mind to something, I can finish it within a week. If I get another idea, it takes me months to finish it. However, I seem to be on a roll with this one, so here's another chapter. Thanks for the faves/follows I got with last chapter!

**Disclaimer: **I don't own Sherlock; the BBC does. Also, thank you to Ariane DeVere on livejournal, who's transcripts of the episodes are highly useful. Quotes may be taken from the actual episodes.

* * *

**Chapter Three**

**The Assisting of You**

* * *

Later Molly called in to quit her job, and returned the keys to her flat. She took her small selection of belongings back to Baker Street, and Sherlock didn't say a word about it. He simply sat in his chair, going through files on his laptop. She stood in the kitchen, drinking coffee. She hadn't had coffee in a while.

"Molly," he called over to her. She looked up, somewhat nervously. "Would you… Would you like to… solve crimes?" Molly frowned, then shrugged. He shut the laptop lid and stood up, making his way over to the door. She frowned. Had he been wearing his coat a moment ago? He must've been, because he was wearing it now, but it certainly hadn't seemed so before.

She sighed, abandoned her coffee and threw on her coat. She slipped her phone into her pocket. It was turned off she made sure it was- but she felt safer with it on her. With a quick glance around the flat, she followed Sherlock out of the door.

* * *

First they went to an underground room with Lestrade, where they found and old skeleton that wasn't really old at all. Molly enjoyed using her knowledge again, even if she had tried so hard to shut them out before now.

This was different, though. Maybe now that Sherlock was back, he would protect her, and she wouldn't have to do it again. She hoped to God that were true, even if she didn't really believe in God.

* * *

Mycroft Holmes was thinking on the return of old faces. First came his brother- the brother he knew to be dead- perfectly well. Yet he had no explanation as to why he had gone. What had he been doing for two years? It was not like his brother to hide. Or to keep an accomplishment to himself. To Sherlock, successfully faking his death would somehow be an accomplishment. So why hide what he had been doing?

He shook his head and leafed through his brother's file, on the desk in front of him. It contained all the information Mycroft had on him, including the results of the autopsy. That had been run by Molly Hooper… Molly Hooper. Had she been in on it, too? She had been trying to 'fly low', so to speak, these past two years. She'd changed her phone number, moved several times each year, and cut off all contact with her old friends. She'd even quit her job, and taken on five others since then, each one completely different.

Maybe Molly Hooper could give him some answers.

* * *

"The train never stops, and a man vanishes," Howard proclaimed, sitting back. "Good, innit?"

"I know that face," Sherlock muttered to himself, and turned around and walked away, apparently lost in thought. Molly turned to Howard with a forced smile.

"Uh, sorry about him," she said. "He's like that sometimes. He'll, uh, get back to you." Howard nodded. Not quite knowing what to do, Molly gave an awkward little wave and went to join Sherlock on the stairway.

"The journey between those stations usually takes five minutes. That journey took ten minutes – ten minutes to get from Westminster to St James's Park. So I'm going to need maps – lots of maps, older maps, all the maps."

"Right," Molly agreed.

"Fish and chips?"

* * *

John stood outside the Baker Street flat. Mary had told him to "stop moping and go visit him"- whatever that meant. He was here nonetheless, though, heading towards the front door. As he took a step forwards a man rudely bumped into him; John frowned after him.

"'Scuse you," he called. At that moment he felt a hand grab his wrist and a needle plunge into his neck. He cried out, trying to grab at his attacker, but already the drugs were taking effect. His struggles weakened and he was forced onto the floor, the world a muddled mess. Moments later, he succumed to the darkness.

* * *

Mary walked down the street. John had been at Sherlock's for three hours; easily enough time to have sorted things out. As she turned onto Baker Street, her phone beeped in her pocket. She fished it out and removed her glove to access the whole text.

_Save souls now!_

_John or James Watson?_

_Saint or Sinner?_

_James or John?_

_The more is Less?_

She read it once, then read it again. The third time she read it she realised what it was: a skip code.

_**Save**__ souls now!_

_**John**__ or James __**Watson**__?_

_**Saint**__ or Sinner?_

_**James**__ or John?_

_**The**__ more is __**Less**__?_

Paling, she hurried off down the street, and rapped on the door. When the landlady opened it, she pushed past her, and made her way up the stairs.

"Sorry- I-I think someone's got John- John Watson?" The door to 221B opened, and Sherlock appeared, a bag of crisps in his hand. Behind him hovered a blonde-haired woman, who looked far too pale and thin to be healthy.

"Hang on! Who are you?" Mrs Hudson asked.

"Oh, I'm his fiancee," Mary replied, running up to Sherlock. Mrs Hudson seemed pleasantly surprised.

"Mary? What's wrong?" he asked her. Mary pulled out her phone and showed him the message.

"Someone sent me this. At first I thought it was just spam, but it's not. It's a skip code." The blonde leaned over her shoulder and read it.

"First word, then every third," Sherlock mumbled thoughtfully.

"Save John Watson. St James the Less," the blonde read. "St James the Less?"

"It's a church," Sherlock replied. "Now!" He hurried down the stairs. Mary raced after him, and the blonde followed. "Did you come in the car?" Sherlock asked. Mary nodded, and he marched out into the road before shaking his head. "It's too slow!" he exclaimed as a car roared past.

"What are we waiting for?" Mary hollered over the sound of the traffic.

"This," Sherlock replied, holding his hand out in front of an approaching motorcycle. Two minutes later the startled couple was ambling away down the street, and Sherlock was handing the helmets to the girls. "Go on, I'll meet you there," he ordered, before jogging away down the street.

Mary hooked her leg over the motorbike, and the blonde climbed on in front.

"I'm Molly," the blonde introduced herself, before revving the engine and causing the bike to shoot down the road. Mary turned her head to watch Sherlock as he jogged down the street. As they were turning the corner, she thought she saw him vanish, but she must've been mistaken. People couldn't vanish, after all.

* * *

**A/N: **Reviews? Please? Also, anything you'd like to see in later chapters?


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